Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1486320314

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:65661369 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000008 (2/264690, TOPMED)
C=0.000014 (2/140240, GnomAD)
C=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DENND4A : 3 Prime UTR Variant
SLC24A1 : 500B Downstream Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 10680 T=1.00000 C=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 T=1.00 C=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 T=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 466 T=1.000 C=0.000 1.0 0.0 0.0 N/A


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.999992 C=0.000008
gnomAD - Genomes Global Study-wide 140240 T=0.999986 C=0.000014
gnomAD - Genomes European Sub 75924 T=0.99997 C=0.00003
gnomAD - Genomes African Sub 42054 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13662 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3130 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2148 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 10680 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 6962 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2294 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 466 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 108 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 94 T=1.00 C=0.00
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 15 NC_000015.10:g.65661369T>C
GRCh37.p13 chr 15 NC_000015.9:g.65953707T>C
SLC24A1 RefSeqGene NG_031968.2:g.54965T>C
Gene: DENND4A, DENN domain containing 4A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DENND4A transcript variant 1 NM_001144823.2:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant 2 NM_005848.4:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant 3 NM_001320835.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant 4 NM_001376919.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant 5 NM_001376920.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X1 XM_047432086.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X2 XM_047432087.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X3 XM_047432088.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X4 XM_047432089.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X5 XM_047432090.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X6 XM_047432091.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X7 XM_047432092.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X8 XM_047432093.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X9 XM_005254120.6:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X10 XM_047432094.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X11 XM_047432095.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X12 XM_047432096.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X13 XM_047432097.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X14 XM_047432098.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X15 XM_047432099.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X16 XM_047432100.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X17 XM_047432101.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X18 XM_047432102.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X19 XM_047432103.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X20 XM_047432104.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X21 XM_047432105.1:c.*482= N/A 3 Prime UTR Variant
DENND4A transcript variant X22 XM_011521156.4:c. N/A Genic Downstream Transcript Variant
DENND4A transcript variant X23 XM_047432106.1:c. N/A Genic Downstream Transcript Variant
Gene: SLC24A1, solute carrier family 24 member 1 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
SLC24A1 transcript variant 5 NM_001301033.2:c. N/A Downstream Transcript Variant
SLC24A1 transcript variant 2 NM_001254740.2:c. N/A N/A
SLC24A1 transcript variant 3 NM_001301031.1:c. N/A N/A
SLC24A1 transcript variant 4 NM_001301032.1:c. N/A N/A
SLC24A1 transcript variant 1 NM_004727.3:c. N/A N/A
SLC24A1 transcript variant X13 XM_011522222.4:c. N/A Downstream Transcript Variant
SLC24A1 transcript variant X12 XM_047433330.1:c. N/A Downstream Transcript Variant
SLC24A1 transcript variant X16 XM_047433333.1:c. N/A Downstream Transcript Variant
SLC24A1 transcript variant X17 XM_047433334.1:c. N/A Downstream Transcript Variant
SLC24A1 transcript variant X21 XM_047433338.1:c. N/A Downstream Transcript Variant
SLC24A1 transcript variant X22 XM_005254781.5:c. N/A N/A
SLC24A1 transcript variant X17 XM_006720768.5:c. N/A N/A
SLC24A1 transcript variant X1 XM_011522219.2:c. N/A N/A
SLC24A1 transcript variant X8 XM_011522221.4:c. N/A N/A
SLC24A1 transcript variant X23 XM_011522226.4:c. N/A N/A
SLC24A1 transcript variant X10 XM_017022724.3:c. N/A N/A
SLC24A1 transcript variant X18 XM_017022725.3:c. N/A N/A
SLC24A1 transcript variant X2 XM_024450103.2:c. N/A N/A
SLC24A1 transcript variant X3 XM_024450104.2:c. N/A N/A
SLC24A1 transcript variant X4 XM_024450105.2:c. N/A N/A
SLC24A1 transcript variant X6 XM_047433325.1:c. N/A N/A
SLC24A1 transcript variant X7 XM_047433326.1:c. N/A N/A
SLC24A1 transcript variant X9 XM_047433327.1:c. N/A N/A
SLC24A1 transcript variant X11 XM_047433328.1:c. N/A N/A
SLC24A1 transcript variant X14 XM_047433331.1:c. N/A N/A
SLC24A1 transcript variant X15 XM_047433332.1:c. N/A N/A
SLC24A1 transcript variant X19 XM_047433335.1:c. N/A N/A
SLC24A1 transcript variant X20 XM_047433336.1:c. N/A N/A
SLC24A1 transcript variant X24 XM_047433339.1:c. N/A N/A
SLC24A1 transcript variant X5 XR_007064494.1:n. N/A Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= C
GRCh38.p14 chr 15 NC_000015.10:g.65661369= NC_000015.10:g.65661369T>C
GRCh37.p13 chr 15 NC_000015.9:g.65953707= NC_000015.9:g.65953707T>C
SLC24A1 RefSeqGene NG_031968.2:g.54965= NG_031968.2:g.54965T>C
DENND4A transcript variant X9 XM_005254120.6:c.*482= XM_005254120.6:c.*482A>G
DENND4A transcript variant X3 XM_005254120.5:c.*482= XM_005254120.5:c.*482A>G
DENND4A transcript variant X3 XM_005254120.4:c.*482= XM_005254120.4:c.*482A>G
DENND4A transcript variant X4 XM_005254120.3:c.*482= XM_005254120.3:c.*482A>G
DENND4A transcript variant X2 XM_005254120.2:c.*482= XM_005254120.2:c.*482A>G
DENND4A transcript variant X2 XM_005254120.1:c.*482= XM_005254120.1:c.*482A>G
DENND4A transcript variant 2 NM_005848.4:c.*482= NM_005848.4:c.*482A>G
DENND4A transcript variant 2 NM_005848.3:c.*482= NM_005848.3:c.*482A>G
DENND4A transcript variant 1 NM_001144823.2:c.*482= NM_001144823.2:c.*482A>G
DENND4A transcript variant 1 NM_001144823.1:c.*482= NM_001144823.1:c.*482A>G
DENND4A transcript variant X4 XM_047432089.1:c.*482= XM_047432089.1:c.*482A>G
DENND4A transcript variant X8 XM_047432093.1:c.*482= XM_047432093.1:c.*482A>G
DENND4A transcript variant X10 XM_047432094.1:c.*482= XM_047432094.1:c.*482A>G
DENND4A transcript variant X12 XM_047432096.1:c.*482= XM_047432096.1:c.*482A>G
DENND4A transcript variant X1 XM_047432086.1:c.*482= XM_047432086.1:c.*482A>G
DENND4A transcript variant X5 XM_047432090.1:c.*482= XM_047432090.1:c.*482A>G
DENND4A transcript variant 3 NM_001320835.1:c.*482= NM_001320835.1:c.*482A>G
DENND4A transcript variant X17 XM_047432101.1:c.*482= XM_047432101.1:c.*482A>G
DENND4A transcript variant X19 XM_047432103.1:c.*482= XM_047432103.1:c.*482A>G
DENND4A transcript variant X2 XM_047432087.1:c.*482= XM_047432087.1:c.*482A>G
DENND4A transcript variant X6 XM_047432091.1:c.*482= XM_047432091.1:c.*482A>G
DENND4A transcript variant X13 XM_047432097.1:c.*482= XM_047432097.1:c.*482A>G
DENND4A transcript variant X3 XM_047432088.1:c.*482= XM_047432088.1:c.*482A>G
DENND4A transcript variant X14 XM_047432098.1:c.*482= XM_047432098.1:c.*482A>G
DENND4A transcript variant X7 XM_047432092.1:c.*482= XM_047432092.1:c.*482A>G
DENND4A transcript variant 4 NM_001376919.1:c.*482= NM_001376919.1:c.*482A>G
DENND4A transcript variant X11 XM_047432095.1:c.*482= XM_047432095.1:c.*482A>G
DENND4A transcript variant X20 XM_047432104.1:c.*482= XM_047432104.1:c.*482A>G
DENND4A transcript variant X16 XM_047432100.1:c.*482= XM_047432100.1:c.*482A>G
DENND4A transcript variant 5 NM_001376920.1:c.*482= NM_001376920.1:c.*482A>G
DENND4A transcript variant X15 XM_047432099.1:c.*482= XM_047432099.1:c.*482A>G
DENND4A transcript variant X18 XM_047432102.1:c.*482= XM_047432102.1:c.*482A>G
DENND4A transcript variant X21 XM_047432105.1:c.*482= XM_047432105.1:c.*482A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2936091507 Nov 08, 2017 (151)
2 TOPMED ss4995043795 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000015.10 - 65661369 Apr 27, 2021 (155)
4 TopMed NC_000015.10 - 65661369 Apr 27, 2021 (155)
5 ALFA NC_000015.10 - 65661369 Apr 27, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2936091507 NC_000015.9:65953706:T:C NC_000015.10:65661368:T:C (self)
472114874, 210589455, 1475558850, ss4995043795 NC_000015.10:65661368:T:C NC_000015.10:65661368:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1486320314

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top▲ Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post820+afb47a3d